Find research datasets worth reusing

opencc-zeroApr 2022View details →

FIG. S11. — Boxplot comparing M3 length among different Late Miocene Eurasian Palaeotragus Gaudry, 1861 in The Vallesian large Palaeotragus Gaudry, 1861 (Mammalia: Giraffidae) from Northern Greece

FIG. S11. — Boxplot comparing M3 length among different Late Miocene Eurasian Palaeotragus Gaudry, 1861 forms.

A comparative analysis testing Werner's theory of complex life cycles

A popular theoretical model for explaining the evolution of complex life cycles was provided by Earl Werner. The theory predicts the size at which an individual should switch stages to maximise growth rate relative to mortality rate across the life history. Werner's theory assumes that body size does not change during the transition from one phase to another (e.g. from larva to adult)—a key assumption that has not been tested systematically but could alter the predictions of the model. We quantified how growth rate and mass change across larval stages and metamorphosis for 105 species of fish, amphibians, insects, crustaceans and molluscs Across all taxonomic groups, we found support for Werner's assumption that growth rates are maintained or increase around transitions. We found that changes in growth and mass were greatest during metamorphosis, and change in growth correlated with development time. Importantly, most species either gained or lost mass when switching to a new stage—a direct contradiction of Werner's assumption. When we explored the consequences of energy loss and gain in a numerical model, we found that individuals should switch stages at a larger and smaller size, respectively, relative to what Werner's standard theory predicts. Our results suggest that while there is support for Werner's assumption regarding growth rates, mass changes profoundly alter the timing of transitions that are predicted to maximise fitness, and therefore the original model omits an important component that may contribute to the evolution of complex life cycles. Future studies should test for conditions that alter the costs of transitions, so that we can have a better understanding of how mass loss or gain affects fitness.

The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships

Sanicula (Apiaceae subfamily Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five Sanicula species (S. flavovirens, S. giraldii, S. lamelligera, S. odorata, and S. rubriflora) were sequenced and compared to the previously published S. orthacantha plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA, and 8 rRNA genes. Loci rpl2, matK, psbA, and ycf1 are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup Hydrocotyle (Araliaceae) reveal sectional relationships in Sanicula different from the traditional classification system, support the monophyly of Apioideae and its sister group relationship to Saniculoideae, and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. Sanicula orthacantha and S. chinensis form a clade sister group to S. lamelligera and S. odorata, consecutively. These four species comprise a clade sister group to the clade of S. rubriflora and S. flavovirens, with this entire group sister to S. giraldii. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic, and population-level studies of Sanicula.

Unexpected morphological diversity in ancient dogs compared to modern relatives

Dogs are among the most variable species today, but little is known about the morphological variability in the early phases of their history. The Neolithic transition to farming may have resulted in an early morphological diversification as a result of changes in the anthropic environment or intentional selection on specific morphologies. Here, we explore the variability and modularity in mandible form by comparing 525 dog mandibles from European archaeological sites ranging from 8,100 to 3,000 cal. BC to a reference sample of modern dogs, wolves, and dingoes. We use three-dimensional geometric morphometrics to quantify the form of complete and fragmented mandibles. We demonstrate that an important morphological variability already existed before the Bronze Age in Europe, yet the largest, smallest, most brachycephalic or dolichocephalic extant dogs have no equivalent in the archaeological sample, resulting in a lower variation compared to modern relatives. The covariation between the anterior and posterior parts of the mandible is lower in archaeological dogs, suggesting a low degree of intentional human selection in early periods. The mandible of modern and ancient dogs differs in functionally important areas, possibly reflecting differences in diet, competition, or the implication of ancient dogs in hunting or defense.

Comparative physiology of canopy tree leaves in evergreen and deciduous forests in lowland Thailand

Three major forest types in lowland Thailand and its adjacent parts in Southeast Asia are mixed deciduous forest (MDF), dry dipterocarp forest (DDF) and dry evergreen forest (DEF). We report the leaf physiology of canopy trees in these forests. The leaf mass-based photosynthetic rates (Amax), stomatal conductance (Gmax) and photosynthetic nitrogen use efficiency were significantly different between the deciduous forests (MDF and DDF) and the evergreen forest (DEF). The canopy trees of MDF with thick, eutrophic soils had the highest intrinsic water use efficiency (Amax/Gmax) among the forest types. Forest-to-forest variations in leaf mass area were related to different nutrient use strategies (less vs. more conservative) associated with different soil nutrients rather than with leaf phenology/longevity. In the interspecific variations within each forest, Amax in MDF and DEF was limited by foliar phosphate, whereas that in DDF was limited by foliar nitrogen. The close association between leaf physiology and soil properties suggests that climate change and increasing human impacts will disrupt this association, leading to forest degradation and dysfunction.

Comparative physiology of canopy tree leaves in evergreen and deciduous forests in lowland Thailand

The major forest types in lowland Thailand and its adjacent parts in Southeast Asia with the distinct dry season are the mixed deciduous forest (MDF), dry dipterocarp forest (DDF) and dry evergreen forest (DEF). We report the first comprehensive data set in leaf physiology of canopy trees in these three forest types and clarify adaptive functional differences of woody plants among three forests. Unlike temperate forests, the forest variations in leaf mass per area (LMA) were related to nutrient use strategies (less vs. more conservative) associated with soil nutrients rather than with leaf phenology (evergreen vs. deciduous). In the interspecific variations within each forest, Amax in MDF and DEF was limited by foliar phosphate, whereas that in DDF was limited by foliar nitrogen. The close association between leaf physiology and soil properties suggests that climate change and increasing human impacts will disrupt this association, leading to forest degradation and dysfunction.

opencc-by-4.0Jun 2022View details →

Core bibliometric Covid19 and comparable research dataset and code for the study "From intent to impact: Investigating the effects of open sharing commitments"

This document provides the underlying dataset for the bibliometric component for the 2022 study "From intent to impact: Investigating the effects of open sharing commitments" by Research Consulting and Science-Metrix. Before reproducing the study findings or re-using the underlying datasets for other purposes, please cautiously review their limitations in the study's technical annex and main report, available at: https://zenodo.org/communities/data-sharing-in-public-health-emergencies/  Particularly, note that there is an error rate in attribution of signatory status to journal publications and preprints; in their location within specific thematic disease-based areas; or computing of dimension such as identification of data availability statement sections; identification of data depisition mentions within data availability statement sections; or matching of preprints and journal publications. These error rates are expected and have been estimated, please consult the technical report for full details.   Definition of data fields is provided is the table below: <table> <tbody> <tr> <td>Column name </td> <td>Definition</td> </tr> <tr> <td>document_type</td> <td>preprint or journal publication</td> </tr> <tr> <td>doi</td> <td>digital object identifier</td> </tr> <tr> <td>arxiv_id</td> <td>arXiv preprint server's unique identifier for its preprints</td> </tr> <tr> <td>ssrn_id</td> <td>SSRN preprint server's unique identifier for its preprints. Note that some of these IDs are contained within the DOIs also assigned to some (but not all) SSRN preprints , in the form of "10.2139/ssrn." + 'ssrn_id'</td> </tr> <tr> <td>coalesce_id</td> <td>coalesce function applied to the DOI, arxiv_id and ssrn_id. Redundant for journal publications.</td> </tr> <tr> <td>preprint_server</td> <td>Preprint platform on which a preprint has been published, restricted to arXiv, bioRxiv, medRxiv and SSRN for this study.</td> </tr> <tr> <td>journal_title</td> <td>Publishing journal name in the case of a journal publication.</td> </tr> <tr> <td>year</td> <td>The set is restricted to 2020 and 2021 for Covid19 preprints and journal publications. HVRD journal publications restricted to 2018-2019. HVRD preprints were restricted to 2020-2021 instead, to compensate for the lac of year-normalization for preprints, and generally better control findings against the launch of medRxiv in 2019.</td> </tr> <tr> <td>publication_title</td> <td>Title of the individual journal publication or preprint, not that of the publishing journal or preprint server.</td> </tr> <tr> <td>authors</td> <td>First 100 researchers that appear as authors of a preprint or journal publication. These are not parsed and provided for qualitative validation or  assessments rather than for further quantitative treatment.</td> </tr> <tr> <td>Covid19</td> <td>Journal publications or preprints are coded 1 if they has been identified as falling into this thematic area through our queries (see the technical annex), 0 otherwise</td> </tr> <tr> <td>HVRD</td> <td>Human viral respiratory disease, the thematic area considered to be the closest to Covid19. Journal publications or preprints are coded 1 if they has been identified as falling into this thematic area through our queries (see the technical annex), 0 otherwise</td> </tr> <tr> <td>Journal_sig</td> <td>Journal publications where the publishing journal and/or its publishing house are Joint Statement signatories. Coded as 1 if they are signatories, 0 if not signatory, null if status could not be determined due to insufficient metadata. Not that all preprint servers included in this study are Joint Statement signatories. This category was fully removed from the models for preprints, rather than all preprints being assigned automatic signatory status.</td> </tr> <tr> <td>RPO_sig</td> <td>Journal publications and preprints where at least one author is affiliated with at least one research performing organization that is a Joint Statement signatory. Coded as 1 ifor signatory, 0 if not signatory, null if status could not be determined due to insufficient metadata.</td> </tr> <tr> <td>Funder_sig</td> <td>Journal publications and preprints where at least one funder supporting the research is a Joint Statement signatory. Coded as 1 ifor signatory, 0 if not signatory, null if status could not be determined due to insufficient metadata. Although funding is attributed to researchers rather than publications, funding metadata is more readily available at the second level. This approach also captures the flexible usage of financial resources that researchers may make accross mulitple concurrently ongoing research projects.</td> </tr> <tr> <td>overton_norm</td> <td>Year and subfield-normalized binary score of whether the journal publications has been cited by one or more policy-related documents from the Overton database. Null scores for journal publications not covered by the database.</td> </tr> <tr> <td>overton</td> <td>Normalizations being unable for preprints, binary score of whether the preprint has been cited by one or more policy-ralated documents from the Overton database. Null scores for preprints not covered by the database.</td> </tr> <tr> <td>daswriting_binary</td> <td>Binary score capturing identification of a data availability statement in the journal publication or preprint using the queries presented in the technical annex. Null scores are for publications and preprints where records of full texts were unavailable for text mining, or were this analysis could not be performed due to licensing restrictions. </td> </tr> <tr> <td>deposition_binary</td> <td>Binary score capturing identification of a data availability statement and data deposition mention therein in the journal publication or preprint using the queries presented in the technical annex. Null scores are for publications and preprints where records of full texts were unavailable for text mining, or were this analysis could not be performed due to licensing restrictions. </td> </tr> <tr> <td>is_oa</td> <td>Binary score capturing OA or free-to-read (also so-calleod "bronze OA" and "green OA") status of journal publications. Unpaywall categories have been used in a mutually exclusive implementation, with the best (gold > hybrid>bronze>green) possible applicable category being retained. Null scores for journal publications not covered in our Unpaywall dataset. Scores of 0 denote journal publications not available under an OA or free-to-read category.</td> </tr> <tr> <td>is_gold</td> <td>as above</td> </tr> <tr> <td>is_hybrid</td> <td>as above</td> </tr> <tr> <td>is_bronze</td> <td>as above</td> </tr> <tr> <td>is_green</td> <td>as above</td> </tr> <tr> <td>matched_journal_binary</td> <td>For preprints, whether one or more matching journal publications could be identified using the queries identified in the technical, or preprint servers' own lists of preprint-journal publication matches. Null scores for preprints with insufficient metadata information to perform the matching operation.</td> </tr> <tr> <td>matched_journal_doi</td> <td>For those preprints with or more matching journal publications, the DOI(s) of the matching journal publication(s). Note that some of the maching journal publications identified do not have DOIs.</td> </tr> <tr> <td>matched_preprint_binary</td> <td>For journal publications, whether one or more matching preceding preprints could be identified using the queries identified in the technical annex, or preprint servers' own lists of preprint-journal publication matches. Null scores for journal publications without sufficient metadata to run the analysis.</td> </tr> <tr> <td>matched_preprint_id</td> <td>For those journal publications preceded with one or more arXiv, bioRxiv, medRxiv or SSRN preprints, the DOI(s), arXiv ID and/or SSRN ID of the matching preprint(s). </td> </tr> <tr> <td>hasdoi</td> <td>Only journal publications with DOIs were retained in the core quantitative analyses.</td> </tr> <tr> <td>hasacknowledgements</td> <td>Only journal publications with funding acknowledgements (to determine funding-based signatory status) were retained in the core quantitative analyses.</td> </tr> <tr> <td>funder_array</td> <td>Array (but cast as string) of names of the funders on the basis of whose idenitification signatory status has been attributed, where relevant. Null if non-signatory or unknown signatory status.</td> </tr> <tr> <td>RPO_array</td> <td>Array (but cast as string) of names of the research performing organizations on the basis of whose idenitification signatory status has been attributed, where relevant. Null if non-signatory or unknown signatory status.</td> </tr> <tr> <td>DAS_excerpt</td> <td>Journal publication or preprint text excerpt on which succesful identifcation of data availability statements and/or data deposition mentions have been made. Null both where the query could not be run at all, or where the query was negative.</td> </tr> <tr> <td>big5</td> <td>Journal publication published in a journal owned by one of the following five publishing houses: Elsevier, Sage, Springer Nature, Taylor-Francis, Wiley.</td> </tr> <tr> <td>LMIC</td> <td>Journal publication whose authors include at least one researcher affiliated with at least one institution located in a lower-middle income country as defined by the World Bank</td> </tr> <tr> <td>LIC</td> <td>Journal publication whose authors include at least one researcher affiliated with at least one institution located in a low income country as defined by the World Bank</td> </tr> <tr> <td>SouthNorth</td> <td>Journal publication whose authors include at least one researcher affiliated with at least one institution located in a upper-middle income country, a lower-middle income country, or a low income country as defined by the World Bank; as well as at least one researcher affiliated with at least one institution located in a high income country. For the purpose of this indicator, Sicnece-Metrix exceptionally includes China and Bulgaria in the list of high income countries.</td> </tr> <tr> <td>DID_allauthors_OR</td> <td>Journal publication is included in the difference-in-difference model defining signatory publication as EITHER holding journal-based signatory status OR funding-based signatory status, and where no filter has been applied to control for author-level biases.</td> </tr> <tr> <td>DID_authorcontrol_OR</td> <td>Journal publication is included in the difference-in-difference model defining signatory publication as EITHER holding journal-based signatory status OR funding-based signatory status, and where a filter has been applied to control for author-level biases.</td> </tr> <tr> <td>DID_authorcontrol_AND</td> <td>Journal publication is included in the difference-in-difference model defining signatory publication as holding journal-based signatory status AND funding-based signatory status, and where a filter has been applied to control for author-level biases.</td> </tr> <tr> <td>DID_allauthors_AND</td> <td>Journal publication is included in the difference-in-difference model defining signatory publication as holding journal-based signatory status AND funding-based signatory status, and where no filter has been applied to control for author-level biases.</td> </tr> <tr> <td>Preprint_authorcontrol</td> <td>Preprint is included in the the analytical breakdowns where a filter has been applied to control for author-level biases. Note that authors have been kept constant in preprints on the basis of their belonging to all analytical breakdowns in journal publications rather than in preprint-based groups.</td> </tr> </tbody> </table>

opencc-by-4.0Jun 2022View details →

Tiempo de publicación en revistas académicas latinoamericanas. © / Time delay in Latin American academic journals. An international comparative analysis

Cuadros comparativos sobre tiempos de aceptación y de publicación de revistas académicas latinoamericanas (Argentina, Brasil, Chile, Colombia y México) incluidas en Scielo. Comparative tables on acceptance and publication times of Latin American academic journals (Argentina, Brazil, Chile, Colombia and Mexico) included in Scielo.

opencc-zeroNov 2019View details →

Data from: Comparative crystallography suggests Maniraptoran theropod affinities for latest cretaceous European 'geckoid' eggshell

Thin fossil eggshells from Upper Cretaceous deposits of Europe, characterized by nodular ornamentation similar to modern gekkotan eggshells, have mostly been interpreted as gekkotan (='geckoid') in origin. However, in some cases, like the oogenus Pseudogeckoolithus, their theropod affinity was also suggested. The true affinity of these fossil 'geckoid' eggshells remained controversial due to the absence of analytical methods effective in identifying genuine gecko eggshells in the fossil record. In this study, we apply electron backscatter diffraction (EBSD) analysis to latest Cretaceous European 'geckoid' (including Pseudogeckoolithus) eggshells, in comparison with modern gekkotan and theropod (avian) eggshells. Our results show that Pseudogeckoolithus has a definite theropod eggshell-like crystallographic configuration, in clear contrast to that seen in modern geckos. Furthermore, the crystallography of the nodular ornamentation in Pseudogeckoolithus is comparable to that seen in megapode eggshells, but different from that of gecko eggshells, despite superficial morphological similarity. The remarkable morphological similarities between Pseudogeckoolithus and modern gecko eggshells are thus convergent, and the 'gekkotan affinity' hypothesis can be dismissed for Pseudogeckoolithus. This study provides a template for differentiating true gekkotan from dinosaurian eggshells in the fossil record. The potential functional significance of eggshell ornamentation, lost in most modern birds, requires further study, and experimental zoological approach may shed light on this issue. Finally, our results caution about the dangers of using potentially homoplastic eggshell characters in eggshell parataxonomy.

opencc-zeroJul 2022View details →

Data for empirical example in: An effect size for comparing the strength of morphological integration across studies

Understanding how and why phenotypic traits covary is a major interest in evolutionary biology. Biologists have long sought to characterize the extent of morphological integration in organisms, but comparing levels of integration for a set of traits across taxa has been hampered by the lack of a reliable summary measure and testing procedure. Here we propose a standardized effect size for this purpose, calculated from the relative eigenvalue variance, Vrel. First we evaluate several eigenvalue dispersion indices under various conditions, and show that only Vrel remains stable across samples size and the number of variables. We then demonstrate that Vrel accurately characterizes input patterns of covariation, so long as redundant dimensions are excluded from the calculations. However, we also show that the variance of the sampling distribution of Vrel depends on input levels of trait covariation, making Vrel unsuitable for direct comparisons. As a solution, we propose transforming Vrel to a standardized effect size (Z-score) for representing the magnitude of integration for a set of traits. We also propose a two-sample test for comparing the strength of integration between taxa, and show that this test displays appropriate statistical properties. We provide software for implementing the procedure, and an empirical example illustrates its use.

opencc-by-4.0Jul 2022View details →

Far-Ultraviolet Photometric Characteristics of JSC-1A and LMS-1 Lunar Regolith Simulants: Comparative Investigations with Apollo 10084

The .txt files listed here contain the data used for Figure 3 and Supplemental Figure S3 of the paper titled "Far-Ultraviolet Photometric Characteristics of JSC-1A and LMS-1 Lunar Regolith Simulants: Comparative Investigations with Apollo 10084."  The experimentally derived phase curves are contained in the files which have the material name (JSC-1A, LMS-1, or Apollo 10084) followed by the wavelength alone (Lyman-a, 140 nm, 160 nm) in the file name.  All files with "Hapke" in the file name are the Hapke photometric model (Hapke, 2012) fitted phase curves for the associated experimental data.  Two of the JSC-1A files have either "LT38" or "GT150" included in the file name; these are the sieved grain size category data referenced in S3. Also included are .txt files of the data points used in Figure 4 for the JSC-1A and LMS-1 simulants.  These each have "Fig4" in the file name.

opencc-by-4.0Aug 2022View details →

A multicenter randomized phase 4 trial comparing Sodium Picosulphate plus Magnesium Citrate vs Polyethylene Glycol plus Ascorbic Acid for bowel PREparation before COLonoscopy. The PRECOL trial.

This is the database for final analysis of the PRECOL clinical trial, whose abstract follows Background. Adequate bowel preparation before colonoscopy is crucial. Unfortunately, up to 25% of all colonoscopies have inadequate bowel cleansing.  From a patient perspective, bowel preparation is a main obstacle for colonoscopy. Several low-volume bowel preparations have been formulated to provide more tolerable purgative solutions without loss of efficacy. Methods: In this phase 4, randomized, multicenter, two-arm trial, adult outpatients undergoing colonoscopy received either Sodium Picosulphate plus Magnesium Citrate (SPMC) or Polyethylene Glycol plus Ascorbic Acid (PEG-ASC) for bowel preparation. The primary aims were to test quality of bowel cleansing (primary endpoint, scored according the Boston Bowel Preparation Scale) and patient’s acceptance (measured with 6 visual analogue scales). The study was open as for treatment assignment, and blinded for primary endpoint assessment that was done independently on videotaped colonoscopies by 2 endoscopists not aware of study arm. A sample size of 525 patients was calculated to recognize a difference of 10% in the proportion of successes between the arms with a two-sided alpha error of 0·05 and 90% statistical power. Findings: overall 550 subjects (279 assigned to PEG-ASC and 271 assigned to SPMC) represented the analysis population. There was no statistically significant difference in the success rate according to BBPS: 94·4% with PEG-ASC and 95·7% with SPMC (P=0·49). Acceptance and willing to repeat were significantly better for SPMC with all the scales. Compliance was less than full in 6·6% and 9·9% of cases with PEG-ASC and SPMC, respectively (P=0·17). Nausea and meteorism were significantly more bothersome with PEG-ASC than SPMC. There were no serious adverse events in either group. Interpretation. SPMC and PEG-ASC are not different in terms of efficacy, but SPMC is better tolerated than PEG-ASC. SPMC could be used as alternative to low-volume PEG based purgative solutions for bowel preparation. Funding. This research had no financial support. ClinicalTrials.gov NCT01649674; EudraCT 2011—000587—10.

opencc-by-4.0Oct 2021View details →

Supplementary files: A Comparative Study of Active Rock Glaciers Mapped from Geomorphic- and Kinematic-Based Approaches in Daxue Shan, Southeast Tibetan Plateau

Supplement of "A Comparative Study of Active Rock Glaciers Mapped from Geomorphic- and Kinematic-Based Approaches in Daxue Shan, Southeast Tibetan Plateau". The supplementary files provide the outlines and parameters of the rock glaciers inventoried by InSAR-assist kinematic-based approach in the Daxue Shan, Southeast Tibet Plateau.  Based on the Sentinel-1A ascending SAR images acquired between 2015 and 2019, we derived a five-year-long LOS mean velocity map of the study area. We then compiled a rock glacier inventory by synergistically interpreting the InSAR-derived surface displacements and geomorphic features based on Google Earth images.

opencc-zeroAug 2022View details →

Comparing climatic suitability and niche distances to explain populations responses to extreme climatic events

Habitat suitability calculated from Species Distribution Models (SDMs) has been used to assess population performance, but empirical studies have provided weak or inconclusive support to this approach. Novel approaches measuring population distances to niche centroid and margin in environmental space have been recently proposed to explain population performance, particularly when populations experience exceptional environmental conditions that may place them outside of the species niche. Here, we use data of co-occurring species' decay, gathered after an extreme drought event occurring in the SE of the Iberian Peninsula which highly affected rich semiarid shrubland communities, to compare the relationship between population decay (mortality and remaining green canopy) and (1) distances between populations' location and species niche margin and centroid in the environmental space, and (2) climatic suitability estimated from frequently used SDMs (here MaxEnt) considering both the extreme climatic episode and the average reference climatic period before this. We found that both SDMs-derived suitability and distances to species niche properly predict populations performance when considering the reference climatic period; but climatic suitability failed to predict performance considering the extreme climate period. In addition, while distance to niche margins accurately predict both mortality and remaining green canopy responses, centroid distances failed to explain mortality, suggesting that indexes containing information about the position to niche margin (inside or outside) are better to predict binary responses. We conclude that the location of populations in the environmental space is consistent with performance responses to extreme drought. Niche distances appear to be a more efficient approach than the use of climate suitability indices derived from more frequently used SDMs to explain population performance when dealing with environmental conditions that are located outside the species environmental niche. The use of this alternative metrics may be particularly useful when designing conservation measures to mitigate impacts of shifting environmental conditions.

opencc-by-4.0Sep 2022View details →

Comparing the representation of a simple visual stimulus across the cerebellar network [dataset]

This repository contains all the raw data that has been used to generate the figures in the paper "Comparing the representation of a simple visual stimulus across the cerebellar network". To use the dataset, select all 10 .zip files provided here and unpack them simultaneously.   The dataset contains the following folders: <ul> <li>freely_swimming_beh folder contains the data for the freely swimming behavior experiments. Inside, subfolders for each behavioral experiment run can be found, containing the experiment metadata and the behavioral log.</li> <li>flashes folder contains the data for the imaging experiments with the FLASHES protocol. Within this folder, three subfolders can be found with the data for each one of the three different types of imaged cell types (GCs, IONs and PCs). Within those subfolders, a folder for each imaged fish can be found, containing a data dictionary with the extracted ROI traces, and a folder with the experiment metadata.</li> <li>steps folder contains the data for the imaging experiments with the STEPS protocol. Within this folder, three subfolders can be found with the data for each one of the three different types of imaged cell types (GCs, IONs and PCs). Within those subfolders, a folder for each imaged fish can be found, containing a data dictionary with the extracted ROI traces, and a folder with the experiment metadata.</li> <li>fitting folder contains data dictionaries with the results from the model fitting needed to reproduce the manuscript figures.</li> <li>data_dict4decoding_complete.h5 is a dictionary file containing all necessary data to reproduce the decoding experiments.</li> </ul>

opencc-by-4.0Apr 2022View details →

Are Neural Bug Detectors Comparable to Software Developers on Variable Misuse Bugs?

Artifact for "Are Neural Bug Detectors Comparable to Software Developers on Variable Misuse Bugs?" Abstract:  Debugging, that is, identifying and fixing bugs in software, is a central part of software development. Developers are therefore often confronted with the task of deciding whether a given code snippet contains a bug, and if yes, where. Recently, data-driven methods have been employed to learn this task of bug detection, resulting (amongst others) in so called neural bug detectors. Neural bug detectors are trained on millions of buggy and correct code snippets. Given the “neural learning” procedure, it seems likely that neu- ral bug detectors – on the specific task of finding bugs – have a performance similar to human software developers. For this work, we set out to substantiate or refute such a hypothesis. We report on the results of an empirical study with over 100 software developers, targeting the comparison of humans and neural bug detectors. As detection task, we chose a specific form of bugs (variable misuse bugs) for which neural bug detectors have recently made significant progress. Our study shows that despite the fact that neural bug detectors see millions of such misuse bugs during training, software developers – when conducting bug detection as a majority decision – are slightly better than neural bug detectors on this class of bugs. Altogether, we find a large overlap in the performance, both for classifying code as buggy and for localizing the buggy line in the code. In comparison to developers, one of the two evaluated neural bug detectors, however, raises a higher number of false alarms in our study. Content: The artifact includes the following components: <ul> <li> Web UI: The developer survey was performed online in the browser of the participants. For this, we created a custom web interface tailored for our study task. We included both the implementation of the frontend (website) and backend implementation (buisness logic and database) in this artifact. Therefore, it is not only possible to replicate our survey with same interface and a new group of participants but it is also possible to extend the interface for future studies.  </li> <li> Neural bug detectors: We evaluate the performance of the developers against two neural bug detectors. In this artifact, we include the bug detectors (implementation + trained models) and the evaluation script used for producing our results. Besides the replication of our bug detector evaluation, the detectors can also be used in future projects for detecting variable misuse bugs in Java methods. </li> <li> Analysis scripts: After collecting the raw results from the developers and neural bug detectors, we performed several analysis to gain insights how developers and bug detectors compare on the variable misuse task. We include all analysis steps in form of Jupyter notebooks in the artifact. With this, it is possible to reproduce all the figures of our paper.  </li> </ul> In addition, we also provide further artifacts that were successfully evaluated at ASE 2022: ASE 2022 Artifact: <a href="https://doi.org/10.5281/zenodo.6958242">10.5281/zenodo.6958242</a> Virtual machine: <a href="https://doi.org/10.5281/zenodo.6957849">10.5281/zenodo.6957849</a>

opencc-by-4.0Oct 2022View details →

The Supplementary Material for the article entitled "Comparative analysis of global transcriptomes in nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after infecting human intestinal epithelium in vitro"

The Supplementary Material (Additional files 1-5, including Table S1-S4 and Figure S1) for this article.   Table S1. Upregulated genes in Group B versus Groups A and C+D.   Table S2. Downregulated genes in Group B versus Groups A and C+D.   Table S3. The enriched GO terms in Group B versus Groups A and C+D.   Table S4. The enriched KEGG pathways in Group B versus Groups A and C+D.   Figure S1. The enriched GO terms and KEGG pathways in Group B relative to Group A. Bar charts show the enriched GO terms (A) and the enriched KEGG pathways (B) by significance power. Color of bars indicate power of significance and length in x axes of bar indicate number of annotated genes in the particular term of pathway. Cnetplots show the relationship between GO term (C) and KEGG pathways (D). Dot size representing GO terms and KEGG pathways indicates number of significantly changed and its annotated genes. The GO terms or KEGG pathways connected through their common and annotated genes.

opencc-by-4.0Dec 2021View details →

Text-fig. 1. Bivariate diagram of length and width of the upper dentition of selected European small and middle size Amphicyoninae compared with the Tuchořice specimens. a: P4; b: M1; c: M2; d: m1; e: m2. Data from Schlosser (1899, 1904), Thenius (1949), Dehm (1950), Heizmann (1973), Ginsburg (1977, 1989), Peigné (2012). Dotted line – ranges of maximum and minimum values from the average of teeth of Cynelos lemanensis from Ulm (Peigné and Heizmann 2003). Abbreviations: L – length; W – width. in The Amphicyoninae (Amphicyonidae, Carnivora, Mammalia) Of The Early Miocene From Tuchořice, The Czech Republic

Text-fig. 1. Bivariate diagram of length and width of the upper dentition of selected European small and middle size Amphicyoninae compared with the Tuchořice specimens. a: P4; b: M1; c: M2; d: m1; e: m2. Data from Schlosser (1899, 1904), Thenius (1949), Dehm (1950), Heizmann (1973), Ginsburg (1977, 1989), Peigné (2012). Dotted line – ranges of maximum and minimum values from the average of teeth of Cynelos lemanensis from Ulm (Peigné and Heizmann 2003). Abbreviations: L – length; W – width.

opencc-by-4.0Dec 2015View details →

Fig. 7 in Comparative morphology study of the male genitalia in the tribe Astathini from China (Coleoptera: Cerambycidae)

Fig. 7. Median lobe plus median struts of Bacchisa, dorsal view. A–C. R5>2.5. A. B. atritarsis. B. B. comate. C. B. dioica. D–G. R5>2.5. D. B. basalis. E. B. fortunei. F. B. guerryi. G. B. rigida. Scale bar = 0.5 mm.